Project Chess, the report revealed, was created in response to the occasionally “contentious talks” on legal issues the company had with the government. The project was started about five years ago, well before the online communications company was acquired for $8.5 billion by Microsoft in October 2011.

Skype has denied allegations in the past that it willingly co-operates with government agencies such as the National Security Agency (NSA).

“It has been suggested that Skype made changes in its architecture at the behest of Microsoft in order to provide law enforcement with greater access to our users’ communications,” Mark Gillett, corporate vice-president in Microsoft’s Skype division, wrote in a blog post. “False. Skype’s architecture decisions are based on our desire to provide the best possible product to our users.”

“It has been suggested that Skype has recently changed its posture and policies with regard to law enforcement,” he added. “False. The move to supernodes was not intended to facilitate greater law enforcement access to our users’ communications. Skype has had a team of Skype employees to respond to legal demands and requests from law enforcement since 2005.”

The New York Times report also revealed the NSA recruited Facebook chief security officer Max Kelly when he left the employ of the social network in 2010.